I have a question about analyzing time series data.
If you use the formula
design(dds) <- ~ time + treat + time:treat dds <- DESeq(dds, test="LRT", reduced = ~ time)
I understand that you are seeing if treatment causes a change in gene expression at any time point, but for the treated term in the formula, are you finding differences between all treated vs all untreated? Not specifically treated vs untreated at time 0?
It seems like this could cause genes to come back as significantly different because it would look like the sample size is tripled when its actually just the same sample on a different day.
For example, with my own data, I have 3 time points and 2 conditions. If I just compare treated vs untreated using Wald test at time 0, I get ~10 significantly different genes.
If I use the time series analysis to see which genes change over time due to the treatment,
design(dds) <- ~ time + treat + time:treat dds <- DESeq(dds, test="LRT", reduced = ~ time + treat)
I get 0 genes as different.
When I try to see which genes are different at any time point including time 0 due to treatment,
design(dds) <- ~ time + treat + time:treat dds <- DESeq(dds, test="LRT", reduced = ~ time)
I now get almost 400 genes as significantly different.
Could this simply be because I've tripled my data set comparing treated to untreated, or is something else going on?
Here's an example of my colData:
sample | time | treat |
P000D0_S00_gd | 0 | yes |
P000D0_S00_gd | 1 | yes |
P000D0_S00_gd | 2 | yes |
P002D0_S0_gd | 0 | no |
P002D0_S0_gd | 1 | no |
P002D0_S0_gd | 2 | no |
P004D0_S4_gd | 0 | yes |
P004D0_S4_gd | 1 | yes |
P004D0_S4_gd | 2 | yes |
P006D1_S00_gd | 0 | no |
P006D1_S00_gd | 1 | no |
P006D1_S00_gd | 2 | no |
P007D1_S02_gd | 0 | no |
P007D1_S02_gd | 1 | no |
P007D1_S02_gd | 2 | no |
P008D1_merged | 0 | no |
P008D1_merged | 1 | no |
P008D1_merged | 2 | no |
P001D0_merged_gd | 0 | yes |
P001D0_merged_gd | 1 | yes |
P001D0_merged_gd | 2 | yes |
P002D0_S0_gd | 0 | yes |
P002D0_S0_gd | 1 | yes |
P002D0_S0_gd | 2 | yes |
Thanks for your help on this!